Examples with RdfParser org.hl7.fhir.r5.formats.RdfParser used on opensource projects

Example 1 with RdfParser

use of org.hl7.fhir.r5.formats.RdfParser in project kindling by HL7.

the class Publisher method generateCodeSystemRegistry.

private void generateCodeSystemRegistry() throws FileNotFoundException, IOException, Exception {
    XmlParser xml = new XmlParser();
    xml.setOutputStyle(OutputStyle.PRETTY);
    Bundle bnd = (Bundle) xml.parse(new CSFileInputStream(Utilities.path(page.getFolders().srcDir, "namingsystem", "namingsystem-terminologies.xml")));
    for (BundleEntryComponent entry : bnd.getEntry()) {
        NamingSystem ns = (NamingSystem) entry.getResource();
        entry.setFullUrl("http://hl7.org/fhir/NamingSystem/" + ns.getId());
        String url = null;
        for (NamingSystemUniqueIdComponent t : ns.getUniqueId()) {
            if (t.getType() == NamingSystemIdentifierType.URI)
                url = t.getValue();
        }
        if (url != null) {
            if (url.startsWith("http://hl7.org/fhir"))
                page.getDefinitions().addNs(url, "System " + ns.getName(), "terminologies-systems.html#" + url);
            page.getDefinitions().addNs(entry.getFullUrl(), ns.getId(), "terminologies-systems.html#" + url);
        }
    }
    List<String> names = new ArrayList<String>();
    Set<String> urls = new HashSet<>();
    names.addAll(page.getCodeSystems().keys());
    Collections.sort(names);
    for (String n : names) {
        CodeSystem cs = page.getCodeSystems().get(n);
        if (cs != null && !urls.contains(cs.getUrl()) && cs.hasUrl() && !cs.getUrl().startsWith("http://terminology.hl7.org")) {
            urls.add(cs.getUrl());
            if (cs.hasName()) {
                NamingSystem ns = new NamingSystem();
                ns.setId(cs.getId());
                ns.setName(cs.getName());
                ns.setStatus(cs.getStatus());
                if (!ns.hasStatus())
                    ns.setStatus(PublicationStatus.DRAFT);
                ns.setKind(NamingSystemType.CODESYSTEM);
                ns.setPublisher(cs.getPublisher());
                for (ContactDetail c : cs.getContact()) {
                    ContactDetail nc = ns.addContact();
                    nc.setName(c.getName());
                    for (ContactPoint cc : c.getTelecom()) {
                        nc.getTelecom().add(cc);
                    }
                }
                ns.setDate(cs.getDate());
                if (!ns.hasDate())
                    ns.setDate(page.getGenDate().getTime());
                ns.setDescription(cs.getDescription());
                ns.addUniqueId().setType(NamingSystemIdentifierType.URI).setValue(cs.getUrl()).setPreferred(true);
                String oid = CodeSystemUtilities.getOID(cs);
                if (oid != null) {
                    if (oid.startsWith("urn:oid:"))
                        oid = oid.substring(8);
                    ns.addUniqueId().setType(NamingSystemIdentifierType.OID).setValue(oid).setPreferred(false);
                }
                ns.setUserData("path", cs.getUserData("path"));
                bnd.addEntry().setResource(ns).setFullUrl("http://hl7.org/fhir/" + ns.fhirType() + "/" + ns.getId());
            }
        }
    }
    xml.compose(new FileOutputStream(Utilities.path(page.getFolders().dstDir, "namingsystem-terminologies.xml")), bnd);
    cloneToXhtml("namingsystem-terminologies", "Terminology Registry", false, "resource-instance:NamingSystem", "Terminology Registry", null, wg("vocab"));
    xml.setOutputStyle(OutputStyle.CANONICAL);
    xml.compose(new FileOutputStream(Utilities.path(page.getFolders().dstDir, "namingsystem-terminologies.canonical.xml")), bnd);
    JsonParser json = new JsonParser();
    json.setOutputStyle(OutputStyle.PRETTY);
    json.compose(new FileOutputStream(Utilities.path(page.getFolders().dstDir, "namingsystem-terminologies.json")), bnd);
    jsonToXhtml("namingsystem-terminologies", "Terminology Registry", TextFile.fileToString(Utilities.path(page.getFolders().dstDir, "namingsystem-terminologies.json")), "resource-instance:NamingSystem", "Terminology Registry", null, wg("vocab"));
    json.setOutputStyle(OutputStyle.CANONICAL);
    json.compose(new FileOutputStream(Utilities.path(page.getFolders().dstDir, "namingsystem-terminologies.canonical.json")), bnd);
    RdfParser rdf = new RdfParser();
    rdf.setOutputStyle(OutputStyle.PRETTY);
    rdf.compose(new FileOutputStream(Utilities.path(page.getFolders().dstDir, "namingsystem-terminologies.ttl")), bnd);
    ttlToXhtml("namingsystem-terminologies", "Terminology Registry", TextFile.fileToString(Utilities.path(page.getFolders().dstDir, "namingsystem-terminologies.ttl")), "resource-instance:NamingSystem", "Terminology Registry", null, wg("vocab"));
    StringBuilder b = new StringBuilder();
    b.append("<table class=\"grid\">\r\n");
    b.append(" <tr>");
    b.append("<td><b>Name</b></td>");
    b.append("<td><b>Uri</b></td>");
    b.append("<td><b>OID</b></td>");
    b.append("</tr>\r\n");
    for (BundleEntryComponent entry : bnd.getEntry()) {
        NamingSystem ns = (NamingSystem) entry.getResource();
        String uri = "";
        String oid = "";
        for (NamingSystemUniqueIdComponent id : ns.getUniqueId()) {
            if (id.getType() == NamingSystemIdentifierType.URI)
                uri = id.getValue();
            if (id.getType() == NamingSystemIdentifierType.OID)
                oid = id.getValue();
        }
        String link = "terminologies-systems.html#" + uri;
        if (ns.getUserData("path") != null)
            link = ns.getUserString("path");
        b.append(" <tr>");
        b.append("<td><a href=\"" + link + "\">" + Utilities.escapeXml(ns.getName()) + "</a></td>");
        b.append("<td>" + Utilities.escapeXml(uri) + "</td>");
        b.append("<td>" + Utilities.escapeXml(oid) + "</td>");
        b.append("</tr>\r\n");
    }
    b.append("</table>\r\n");
    String html = TextFile.fileToString(page.getFolders().templateDir + "template-example.html").replace("<%example%>", b.toString()).replace("<%example-usage%>", "");
    html = page.processPageIncludes("namingsystem-terminologies.html", html, "resource-instance:NamingSystem", null, bnd, null, "Example", null, null, page.getDefinitions().getWorkgroups().get("fhir"));
    TextFile.stringToFile(html, page.getFolders().dstDir + "namingsystem-terminologies.html");
    cachePage("namingsystem-terminologies.html", html, "Registered Code Systems", false);
}

Example 2 with RdfParser

use of org.hl7.fhir.r5.formats.RdfParser in project kindling by HL7.

the class Publisher method resource2Ttl.

private String resource2Ttl(Resource r) throws Exception {
    ByteArrayOutputStream bytes = new ByteArrayOutputStream();
    IParser rdf = new RdfParser().setOutputStyle(OutputStyle.PRETTY);
    rdf.setSuppressXhtml("Snipped for Brevity");
    rdf.compose(bytes, r);
    bytes.close();
    return new String(bytes.toByteArray());
}

Example 3 with RdfParser

use of org.hl7.fhir.r5.formats.RdfParser in project org.hl7.fhir.core by hapifhir.

the class ToolsHelper method executeJson.

public String executeJson(String[] args) throws IOException, FHIRException {
    FileInputStream in;
    File source = new CSFile(args[1]);
    File dest = new CSFile(args[2]);
    File destc = new CSFile(Utilities.changeFileExt(args[2], ".canonical.json"));
    File destt = new CSFile(args[2] + ".tmp");
    File destr = new CSFile(Utilities.changeFileExt(args[2], ".ttl"));
    if (!source.exists())
        throw new FHIRException("Source File \"" + source.getAbsolutePath() + "\" not found");
    in = new CSFileInputStream(source);
    XmlParser p = new XmlParser();
    Resource rf = p.parse(in);
    JsonParser json = new JsonParser();
    json.setOutputStyle(OutputStyle.PRETTY);
    FileOutputStream s = new FileOutputStream(dest);
    json.compose(s, rf);
    s.close();
    json.setOutputStyle(OutputStyle.CANONICAL);
    s = new FileOutputStream(destc);
    json.compose(s, rf);
    s.close();
    json.setSuppressXhtml("Snipped for Brevity");
    json.setOutputStyle(OutputStyle.PRETTY);
    s = new FileOutputStream(destt);
    json.compose(s, rf);
    s.close();
    RdfParserBase rdf = new RdfParser();
    s = new FileOutputStream(destr);
    rdf.compose(s, rf);
    s.close();
    return TextFile.fileToString(destt.getAbsolutePath());
}

Example 4 with RdfParser

use of org.hl7.fhir.r5.formats.RdfParser in project org.hl7.fhir.core by hapifhir.

the class ToolsHelper method processExamples.

public void processExamples(String rootDir, Collection<String> list) throws FHIRException {
    for (String n : list) {
        try {
            String filename = rootDir + n + ".xml";
            // 1. produce canonical XML
            CSFileInputStream source = new CSFileInputStream(filename);
            FileOutputStream dest = new FileOutputStream(Utilities.changeFileExt(filename, ".canonical.xml"));
            XmlParser p = new XmlParser();
            Resource r = p.parse(source);
            XmlParser cxml = new XmlParser();
            cxml.setOutputStyle(OutputStyle.CANONICAL);
            cxml.compose(dest, r);
            // 2. produce JSON
            source = new CSFileInputStream(filename);
            dest = new FileOutputStream(Utilities.changeFileExt(filename, ".json"));
            r = p.parse(source);
            JsonParser json = new JsonParser();
            json.setOutputStyle(OutputStyle.PRETTY);
            json.compose(dest, r);
            json = new JsonParser();
            json.setOutputStyle(OutputStyle.CANONICAL);
            dest = new FileOutputStream(Utilities.changeFileExt(filename, ".canonical.json"));
            json.compose(dest, r);
            // 2. produce JSON
            dest = new FileOutputStream(Utilities.changeFileExt(filename, ".ttl"));
            RdfParserBase rdf = new RdfParser();
            rdf.compose(dest, r);
        } catch (Exception e) {
            e.printStackTrace();
            throw new FHIRException("Error Processing " + n + ".xml: " + e.getMessage(), e);
        }
    }
}

Example 5 with RdfParser

use of org.hl7.fhir.r5.formats.RdfParser in project org.hl7.fhir.core by hapifhir.

the class JavaCoreGenerator method generate.

private void generate(String version, String src, String dest) throws Exception {
    long start = System.currentTimeMillis();
    Date date = new Date();
    String ap = Utilities.path(src);
    System.out.println("Load Configuration from " + ap);
    Configuration config = new Configuration(ap);
    String pid = VersionUtilities.isR4BVer(version) ? "r4b" : "r5";
    String jid = VersionUtilities.isR4BVer(version) ? "r4b" : "r5";
    FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
    System.out.println("Cache: " + pcm.getFolder());
    System.out.println("Load hl7.fhir." + pid + ".core");
    NpmPackage npm = pcm.loadPackage("hl7.fhir." + pid + ".core", version);
    Definitions master = VersionUtilities.isR4BVer(version) ? DefinitionsLoaderR4B.load(npm) : DefinitionsLoaderR5.load(npm);
    master.fix();
    markValueSets(master, config);
    System.out.println("Load hl7.fhir." + pid + ".expansions");
    Definitions expansions = DefinitionsLoaderR5.load(pcm.loadPackage("hl7.fhir." + pid + ".expansions", version));
    System.out.println("Process Expansions");
    updateExpansions(master, expansions);
    System.out.println("Generate Model");
    System.out.println(" .. Constants");
    JavaConstantsGenerator cgen = new JavaConstantsGenerator(new FileOutputStream(Utilities.path(dest, "src", "main", "java", "org", "hl7", "fhir", jid, "model", "Constants.java")), master, config, date, npm.version(), jid);
    cgen.generate();
    cgen.close();
    System.out.println(" .. Enumerations");
    JavaEnumerationsGenerator egen = new JavaEnumerationsGenerator(new FileOutputStream(Utilities.path(dest, "src", "main", "java", "org", "hl7", "fhir", jid, "model", "Enumerations.java")), master, config, date, npm.version(), jid);
    egen.generate();
    egen.close();
    JavaFactoryGenerator fgen = new JavaFactoryGenerator(new FileOutputStream(Utilities.path(dest, "src", "main", "java", "org", "hl7", "fhir", jid, "model", "ResourceFactory.java")), master, config, date, npm.version(), jid);
    JavaTypeGenerator tgen = new JavaTypeGenerator(new FileOutputStream(Utilities.path(dest, "src", "main", "java", "org", "hl7", "fhir", jid, "model", "ResourceType.java")), master, config, date, npm.version(), jid);
    JavaParserJsonGenerator jgen = new JavaParserJsonGenerator(new FileOutputStream(Utilities.path(dest, "src", "main", "java", "org", "hl7", "fhir", jid, "formats", "JsonParser.java")), master, config, date, npm.version(), jid);
    JavaParserXmlGenerator xgen = new JavaParserXmlGenerator(new FileOutputStream(Utilities.path(dest, "src", "main", "java", "org", "hl7", "fhir", jid, "formats", "XmlParser.java")), master, config, date, npm.version(), jid);
    JavaParserRdfGenerator rgen = new JavaParserRdfGenerator(new FileOutputStream(Utilities.path(dest, "src", "main", "java", "org", "hl7", "fhir", jid, "formats", "RdfParser.java")), master, config, date, npm.version(), jid);
    if (VersionUtilities.isR4BVer(version)) {
        StructureDefinition sd = master.getStructures().get("http://hl7.org/fhir/StructureDefinition/Element");
        genClass(version, dest, date, config, jid, npm, master, jgen, xgen, rgen, sd);
    }
    for (StructureDefinition sd : master.getStructures().getList()) {
        if (sd.getDerivation() == TypeDerivationRule.SPECIALIZATION && sd.getKind() == StructureDefinitionKind.COMPLEXTYPE) {
            if (!Utilities.existsInList(sd.getName(), "Base", "PrimitiveType") && !sd.getName().contains(".") && sd.getAbstract()) {
                genClass(version, dest, date, config, jid, npm, master, jgen, xgen, rgen, sd);
            }
        }
    }
    for (StructureDefinition sd : master.getStructures().getList()) {
        if (sd.getDerivation() == TypeDerivationRule.SPECIALIZATION && sd.getKind() == StructureDefinitionKind.COMPLEXTYPE) {
            if (!Utilities.existsInList(sd.getName(), "Base", "PrimitiveType") && !sd.getName().contains(".") && !sd.getAbstract()) {
                genClass(version, dest, date, config, jid, npm, master, jgen, xgen, rgen, sd);
            }
        }
    }
    if (VersionUtilities.isR4BVer(version)) {
        StructureDefinition sd = master.getStructures().get("http://hl7.org/fhir/StructureDefinition/Resource");
        genClass(version, dest, date, config, jid, npm, master, jgen, xgen, rgen, sd);
    }
    for (StructureDefinition sd : master.getStructures().getList()) {
        if (sd.getDerivation() == TypeDerivationRule.SPECIALIZATION && sd.getKind() == StructureDefinitionKind.RESOURCE) {
            if (!Utilities.existsInList(sd.getName(), "Base", "PrimitiveType") && !sd.getName().contains(".") && sd.getAbstract()) {
                genClass(version, dest, date, config, jid, npm, master, jgen, xgen, rgen, sd);
            }
        }
    }
    for (StructureDefinition sd : master.getStructures().getList()) {
        if (sd.getDerivation() == TypeDerivationRule.SPECIALIZATION && sd.getKind() == StructureDefinitionKind.RESOURCE) {
            if (!Utilities.existsInList(sd.getName(), "Base", "PrimitiveType") && !sd.getName().contains(".") && !sd.getAbstract()) {
                genClass(version, dest, date, config, jid, npm, master, jgen, xgen, rgen, sd);
            }
        }
    }
    System.out.println(" .. Factory");
    fgen.generate();
    fgen.close();
    System.out.println(" .. Types");
    tgen.generate();
    tgen.close();
    System.out.println(" .. JsonParser");
    jgen.generate();
    jgen.close();
    System.out.println(" .. XmlParser");
    xgen.generate();
    xgen.close();
    System.out.println(" .. RdfParser");
    rgen.generate();
    rgen.close();
    System.out.println("Done (" + Long.toString(System.currentTimeMillis() - start) + "ms)");
}